1odg: Difference between revisions

(10 intermediate revisions by the same user not shown)

Line 1:

~~{{Seed}}~~

~~[[Image:1odg.png|left|200px]]~~

<!--

==Very-short-patch DNA repair endonuclease bound to its reaction product site==

~~The line below this paragraph~~, ~~containing~~ "~~STRUCTURE_1odg~~"~~, creates the~~ "~~Structure Box~~" ~~on the page~~.

~~You may change~~ the ~~PDB parameter (which sets~~ the ~~PDB file loaded into~~ the ~~applet~~)

== Structural highlights ==

or ~~the SCENE parameter~~ (~~which sets~~ the ~~initial scene displayed when~~ the ~~page is loaded)~~,

<table><tr><td colspan='2'>[[1odg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ODG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ODG FirstGlance]. <br>

~~or leave~~ the ~~SCENE parameter empty for~~ the ~~default display~~.

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr>

-->

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>

~~{{STRUCTURE_1odg| PDB~~=~~1odg | SCENE~~= }}

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1odg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1odg OCA], [https://pdbe.org/1odg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1odg RCSB], [https://www.ebi.ac.uk/pdbsum/1odg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1odg ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/VSR_ECOLI VSR_ECOLI] Deamination of 5-methylcytosine in DNA results in T/G mismatches. If unrepaired, these mismatches can lead to C-to-C transition mutations. The very short patch (VSP) repair process in E.coli counteracts the mutagenic process by repairing the mismatches in favor of the G-containing strand. This enzyme is an endonuclease that nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue that is mismatched to 2'-deoxyguanosine. The incision is mismatch-dependent and strand-specific.

== Evolutionary Conservation ==

[[Image:Consurf_key_small.gif|200px|right]]

Check<jmol>

<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/od/1odg_consurf.spt"</scriptWhenChecked>

<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>

<text>to colour the structure by Evolutionary Conservation</text>

</jmolCheckbox>

</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1odg ConSurf].

== Publication Abstract from PubMed ==

Very-short-patch repair (Vsr) enzymes occur in a variety of bacteria, where they initiate nucleotide excision repair of G:T mismatches arising by deamination of 5-methyl-cytosines in specific regulatory sequences. We have now determined the structure of the archetypal dcm-Vsr endonuclease from Escherichia coli bound to the cleaved authentic hemi-deaminated/hemi-methylated dcm sequence 5'-C-OH-3' 5'-p-T-p-A-p-G-p-G-3'/3'-G-p-G-p-T-p(Me5)C-p-C formed by self-assembly of a 12mer oligonucleotide into a continuous nicked DNA superhelix. The structure reveals the presence of a Hoogsteen base pair within the deaminated recognition sequence and the substantial distortions of the DNA that accompany Vsr binding to product sites.

~~===VERY~~-~~SHORT~~-~~PATCH~~ DNA ~~REPAIR ENDONUCLEASE BOUND TO ITS REACTION PRODUCT SITE===~~

Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix.,Bunting KA, Roe SM, Headley A, Brown T, Savva R, Pearl LH Nucleic Acids Res. 2003 Mar 15;31(6):1633-9. PMID:12626704<ref>PMID:12626704</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

~~<!--~~

==See Also==

~~The line below this paragraph, {{ABSTRACT_PUBMED_12626704}}, adds the Publication Abstract to the page~~

*[[Endonuclease 3D structures|Endonuclease 3D structures]]

~~(as it appears on PubMed at http://www.pubmed.gov), where 12626704 is the PubMed ID number.~~

== References ==

~~-->~~

~~{{ABSTRACT_PUBMED_12626704}}~~

__TOC__

</StructureSection>

==~~About this Structure~~==

~~1ODG is a 3 chains structure of sequences from~~ [~~http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli~~]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ODG OCA~~].

==~~Reference~~==

<~~ref group="xtra">PMID:12626704<~~/~~ref~~><~~references group="xtra"~~/>

[[Category: Escherichia coli]]

[[Category: Brown, T.]]

[[Category: Large Structures]]

[[Category: Bunting~~, K A.~~]]

[[Category: Brown T]]

[[Category: Headley, A.]]

[[Category: Bunting KA]]

[[Category: Pearl~~, L H.~~]]

[[Category: Headley A]]

[[Category: Roe~~, S M.~~]]

[[Category: Pearl LH]]

[[Category: Savva, R~~.]]~~

[[Category: Roe SM]]

~~[[Category: Dna repai hydrolase]]~~

[[Category: Savva R]]

~~[[Category: Dna repair]]~~

~~[[Category: Endonuclease]]~~

~~[[Category: Metal-binding]]~~

~~[[Category: Nuclease]]~~

~~[[Category: Very short patch repair]]~~

~~[[Category: Zinc]~~]

~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 13:09:10 2009''~~

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1odg.png|left|200px]]
-<!--
+==Very-short-patch DNA repair endonuclease bound to its reaction product site==
-The line below this paragraph, containing "STRUCTURE_1odg", creates the "Structure Box" on the page.
+<StructureSection load='1odg' size='340' side='right'caption='[[1odg]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1odg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ODG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ODG FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1odg|  PDB=1odg  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1odg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1odg OCA], [https://pdbe.org/1odg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1odg RCSB], [https://www.ebi.ac.uk/pdbsum/1odg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1odg ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VSR_ECOLI VSR_ECOLI] Deamination of 5-methylcytosine in DNA results in T/G mismatches. If unrepaired, these mismatches can lead to C-to-C transition mutations. The very short patch (VSP) repair process in E.coli counteracts the mutagenic process by repairing the mismatches in favor of the G-containing strand. This enzyme is an endonuclease that nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue that is mismatched to 2'-deoxyguanosine. The incision is mismatch-dependent and strand-specific.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/od/1odg_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1odg ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Very-short-patch repair (Vsr) enzymes occur in a variety of bacteria, where they initiate nucleotide excision repair of G:T mismatches arising by deamination of 5-methyl-cytosines in specific regulatory sequences. We have now determined the structure of the archetypal dcm-Vsr endonuclease from Escherichia coli bound to the cleaved authentic hemi-deaminated/hemi-methylated dcm sequence 5'-C-OH-3' 5'-p-T-p-A-p-G-p-G-3'/3'-G-p-G-p-T-p(Me5)C-p-C formed by self-assembly of a 12mer oligonucleotide into a continuous nicked DNA superhelix. The structure reveals the presence of a Hoogsteen base pair within the deaminated recognition sequence and the substantial distortions of the DNA that accompany Vsr binding to product sites.
-===VERY-SHORT-PATCH DNA REPAIR ENDONUCLEASE BOUND TO ITS REACTION PRODUCT SITE===
+Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix.,Bunting KA, Roe SM, Headley A, Brown T, Savva R, Pearl LH Nucleic Acids Res. 2003 Mar 15;31(6):1633-9. PMID:12626704<ref>PMID:12626704</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1odg" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12626704}}, adds the Publication Abstract to the page
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12626704 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12626704}}
+__TOC__
+</StructureSection>
-==About this Structure==
-ODG is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ODG OCA].
-==Reference==
-<ref group="xtra">PMID:12626704</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: Brown, T.]]
+[[Category: Large Structures]]
-[[Category: Bunting, K A.]]
+[[Category: Brown T]]
-[[Category: Headley, A.]]
+[[Category: Bunting KA]]
-[[Category: Pearl, L H.]]
+[[Category: Headley A]]
-[[Category: Roe, S M.]]
+[[Category: Pearl LH]]
-[[Category: Savva, R.]]
+[[Category: Roe SM]]
-[[Category: Dna repai hydrolase]]
+[[Category: Savva R]]
-[[Category: Dna repair]]
-[[Category: Endonuclease]]
-[[Category: Metal-binding]]
-[[Category: Nuclease]]
-[[Category: Very short patch repair]]
-[[Category: Zinc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:09:10 2009''